Reads mapping and coverage quality control (QC) files for a sample, summarizes key metrics, and writes a summary table to the output directory.
Usage
SummarizeMapQC(input_dir, prefix, platform, out_dir)
Arguments
- input_dir
Character. Path to the directory containing QC files for the sample.
- prefix
Character. Sample ID and file prefix.
- platform
Character. Sequencing platform, either "wgs" (whole genome sequencing) or "targeted".
- out_dir
Character. Output directory for the summary table.
Value
Invisibly returns a data frame containing the QC summary metrics.
Details
The function reads mapping and coverage QC files from input_dir, extracts key metrics, and writes a summary table to out_dir with the specified prefix. The summary includes metrics relevant to the specified platform.
